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Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

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Abstract

The ever-larger data matrices resulting from continuing improvements in DNA sequencing techniques require faster and more efficient methods of phylogenetic analysis. Here we explore a promising new method, parsimony jackknifing, by analyzing a matrix comprising 2538 sequences of the chloroplast generbcL. The sequences included cover a broad taxonomic range, from cyanobacteria to flowering plants. Several parsimony jackknife analyses were performed, both with and without branch-swapping and multiple random addition sequences: 1) including all positions; 2) including only first and second codon positions; 3) including only third positions; and 4) using only transversions. The best resolution was obtained using all positions. Removal of third positions or transitions led to massive loss of resolution, although using only transversions somewhat improved basal resolution. While branch-swapping improved both resolution and the support found for several groups, most of the groups could be recovered by faster simple analyses. Designed to eliminate groups poorly supported by the data, parsimony jackknifing recognizes 1400 groups on the basis of allrbcL positions. These include major taxa such as green plants, land plants, flowering plants, monocots and eudicots. We include appendices of supported angiosperm families, as well as larger groups.

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Authors and Affiliations

  1. Molecular Systematics Laboratory, Swedish Museum of Natural History, P.O. Box 50007, S-104 05, Stockholm, Sweden

    Mari Källersjö & James S. Farris

  2. Jodrell Laboratory, Royal Botanic Gardens, TW9 3DS, Kew, Richmond, Surrey, UK

    Mark W. Chase & Michael F. Fay

  3. Department of Systematic Botany, Uppsala University, Villavägen 6, S-723 36, Uppsala, Sweden

    Birgitta Bremer & Kåre Bremer

  4. Department of Botany, The Natural History Museum, Cromwell Road, SW7 5BD, London, UK

    Christopher J. Humphries

  5. Botanical Institute, University of Copenhagen, Gothersgade 140, DK-1123, Copenhagen K, Denmark

    Gitte Petersen & Ole Seberg

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  1. Mari Källersjö
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  2. James S. Farris
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  3. Mark W. Chase
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Källersjö, M., Farris, J.S., Chase, M.W. et al. Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Pl Syst Evol 213, 259–287 (1998). https://doi.org/10.1007/BF00985205

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